1##fileformat=VCFv4.2 2##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons."> 3##FILTER=<ID=PASS,Description="Site contains at least one allele that passes filters"> 4##FILTER=<ID=base_qual,Description="alt median base quality"> 5##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor"> 6##FILTER=<ID=contamination,Description="contamination"> 7##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates"> 8##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length"> 9##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic"> 10##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype."> 11##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold"> 12##FILTER=<ID=map_qual,Description="ref - alt median mapping quality"> 13##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD"> 14##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio"> 15##FILTER=<ID=normal_artifact,Description="artifact_in_normal"> 16##FILTER=<ID=numt_chimera,Description="NuMT variant with too many ALT reads originally from autosome"> 17##FILTER=<ID=orientation,Description="orientation bias detected by the orientation bias mixture model"> 18##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals"> 19##FILTER=<ID=position,Description="median distance of alt variants from end of reads"> 20##FILTER=<ID=possible_numt,Description="Allele depth is below expected coverage of NuMT in autosome"> 21##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region"> 22##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only"> 23##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions"> 24##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold"> 25##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> 26##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor"> 27##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> 28##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> 29##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele"> 30##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> 31##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 32##FORMAT=<ID=MBQ,Number=R,Type=Integer,Description="median base quality"> 33##FORMAT=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length"> 34##FORMAT=<ID=MMQ,Number=A,Type=Integer,Description="median mapping quality"> 35##FORMAT=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read"> 36##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> 37##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> 38##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> 39##FORMAT=<ID=POTENTIAL_POLYMORPHIC_NUMT,Number=1,Type=String,Description="Potentially a polymorphic NuMT false positive rather than a real mitochondrial variant."> 40##FORMAT=<ID=SAAF,Number=3,Type=Float,Description="MAP estimates of allele fraction given z"> 41##FORMAT=<ID=SAPP,Number=3,Type=Float,Description="posterior probabilities of the presence of strand artifact"> 42##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output /var/folders/93/_k0rj4yx0j3bmkf8zg0hjv_40000gq/T/filtered6513237016345540631.vcf --mitochondria-mode true --unique-alt-read-count 2 --min-reads-per-strand 1 --min-allele-fraction 0.5 --variant /Users/ahaessly/code/gatk/src/test/resources/org/broadinstitute/hellbender/tools/mutect/mito/unfiltered-with-assb.vcf --reference /Users/ahaessly/code/gatk/src/test/resources/org/broadinstitute/hellbender/tools/mutect/mito/Homo_sapiens_assembly38.mt_only.fasta --disable-sequence-dictionary-validation true --verbosity ERROR --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --max-events-in-region 2 --max-alt-allele-count 1 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 1 --max-n-ratio Infinity --max-numt-fraction 0.85 --contamination-estimate 0.0 --log-snv-prior -13.815510557964275 --log-indel-prior -16.11809565095832 --log-artifact-prior -2.302585092994046 --normal-p-value-threshold 0.001 --min-slippage-length 8 --pcr-slippage-rate 0.1 --distance-on-haplotype 100 --long-indel-length 5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="Unavailable",Date="March 5, 2020 2:28:05 PM EST"> 43##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Filter status for each allele, as assessed by ApplyRecalibration. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles."> 44##INFO=<ID=AS_SB_TABLE,Number=R,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests"> 45##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=String,Description="Number of reads with unique start and mate end positions for each alt at a variant site"> 46##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Posterior probability for alt allele to be due to contamination"> 47##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> 48##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype"> 49##INFO=<ID=GERMQ,Number=A,Type=Float,Description="Posterior probability for alt allele to be germline variants"> 50##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal LOD score"> 51##INFO=<ID=N_ART_LOD,Number=A,Type=Float,Description="log odds of artifact in normal with same allele fraction as tumor"> 52##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig."> 53##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals"> 54##INFO=<ID=POPAF,Number=A,Type=Float,Description="population allele frequencies of alt alleles"> 55##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> 56##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)"> 57##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="None"> 58##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat"> 59##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="None"> 60##INFO=<ID=TLOD,Number=A,Type=Float,Description="LOD score for variant"> 61##Mutect Version=2.1 62##contig=<ID=chrM,length=16569> 63##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS. 64##source=FilterMutectCalls 65##source=Mutect2 66#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 67chrM 152 . T C . strand_bias;strict_strand AS_FilterStatus=strand_bias,strict_strand;AS_SB_TABLE=0,3|0,1556;DP=1582;ECNT=1;OCM=0;POPAF=5.000e-08;TLOD=5266.19 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:POTENTIAL_POLYMORPHIC_NUMT 0/1:3,1556:0.998:2,777:1,779:30,30:16270,369:60,60:42:true 68chrM 263 . A G . PASS AS_FilterStatus=SITE;AS_SB_TABLE=1,0|431,400;DP=858;ECNT=4;OCM=800;POPAF=5.000e-08;TLOD=2641.72 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS 0/1:1,831:0.999:0,403:1,428:10,30:292,305:60,60:32 69chrM 301 . A AC . low_allele_frac;weak_evidence AS_FilterStatus=weak_evidence,low_allele_frac;AS_SB_TABLE=500,149|41,12;DP=680;ECNT=4;OCM=0;POPAF=5.000e-08;TLOD=3.32 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS 0/1:579,53:0.084:243,27:336,26:30,20:309,324:60,60:34 70chrM 302 . A AC,C,ACC . PASS AS_FilterStatus=SITE|weak_evidence,strand_bias,low_allele_frac|strand_bias,strict_strand,low_allele_frac;AS_SB_TABLE=0,5|51,350|60,7|49,0;DP=659;ECNT=4;OCM=0;POPAF=5.000e-08,5.000e-08,5.000e-08;TLOD=891.23,10.66,67.66 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS 0/1/2/3:5,401,67,49:0.768,0.128,0.094:2,163,35,20:3,238,32,29:20,20,30,20:419,316,340,278:60,60,60,60:41,33,38 71chrM 310 . T TC . PASS AS_FilterStatus=SITE;AS_SB_TABLE=0,0|300,358;DP=705;ECNT=4;OCM=0;POPAF=5.000e-08;RPA=5,6;RU=C;STR;TLOD=1974.89 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS 0/1:0,658:1.00:0,273:0,385:0,30:0,311:60,60:33 72chrM 750 . A G . duplicate AS_FilterStatus=duplicate;AS_SB_TABLE=0,1|100,1424;AS_UNIQ_ALT_READ_COUNT=2;DP=1568;ECNT=1;OCM=0;POPAF=5.000e-08;TLOD=5097.90 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:POTENTIAL_POLYMORPHIC_NUMT 0/1:1,1524:0.999:0,728:1,796:2,30:417,335:60,60:40:true 73chrM 802 . A C,ACC . FAIL AS_FilterStatus=weak_evidence,strand_bias,strict_strand|low_allele_frac;AS_SB_TABLE=55,50|0,301|30,37;DP=659;ECNT=4;OCM=0;POPAF=5.000e-08,5.000e-08;TLOD=10.66,891.23 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS 0/1/2:105,301,67:0.636,0.141:2,163,35:3,238,32:20,20,30:419,316,340:60,60,60:41,33 74